Add warning to the top of MultiQC reports if samples are skipped due to low alignment

[ewels]

From @ewels on June 29, 2017 10:4

Although a warning is given in the Nextflow log when a sample is skipped, it's not so obvious after the run is finished and forgotten.

It would be good to add a section to the top of the MultiQC report highlighting any skipped samples. We should be able to do this using a custom content file and kind of trick MultiQC.

For example, call it alerts_mqc.yaml and have something like this (untested):

id: ngi-rnaseq-alerts
section_name: NGI-RNAseq Warnings
description: |
  <div class="alert alert-danger">
    <p><strong>Warning!</strong> 14 samples were halted after alignment due to very low alignment rates.</p>
    <ul>
      <li>Sample 1 (2.3% aligned)</li>
      <li>Sample 2 (0.4% aligned)</li>
    </ul>
  </div>

I'm not quite sure what happens if you don't supply any plot data to Custom Content, so if this doesn't work right away then I'll take a look into the inner-workings of MultiQC.

Copied from original issue: SciLifeLab#139

[ewels]

Example YAML file here, but requires the latest dev version of MultiQC to work.

Can combine with this other new feature to specify where these sections go in the report if necessary.

[drpatelh]

Added this via a custom table to the top of the MultiQC report as you can see in the image below:

Is this ok to close @ewels ?

[apeltzer]

I'd say yes, much better than having nothing in the Report which was the current default until you implemented this :-)